Geology Reference
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advances have been made over the last ten years,
many problems and issues await resolution. It is a
fertile ground for further research.
Virtually all of the microbes listed in these
papers were identified on the basis of culturing
coupled with optical and electron microscopy. Cul-
turing of microbes, however, commonly provides
a very biased view of the total population. Amann
et al. (1995) and Amann et al. (1996), for
example, suggested that less than 1% of microbes
in any given population are culturable by standard
methods. Application of that ratio to the 627 taxa
of microbes listed by Draganov (1977) implies
that the microbial biotas found in caves may com-
prise at least 62 700 taxa! The difficulty of recog-
nition using these methods is compounded by the
fact that microbes are not that diverse in terms of
their morphology as there are limits to the degree
of morphological variance that can be expected
among the morphologically-simple filamentous,
coccoid, or bacilliform architectures of most
microbes (e.g. Barton 2006).
Over the last twenty years or so, methods for the
identification and characterization of microbes have
changed significantly. As a result, microbes are now
typically identified by their chemotaxonomic char-
acters, 16S rRNA gene sequencing, and polyphasic
taxonomy. Such methods allow microbe identifi-
cation without cultivation and places emphasis on
the DNA of the microbes rather than their mor-
phology and/or culture conditions. Application of
these methods to microbial biotas collected from
caves has revealed diverse, complex biotas, as is
shown by the following examples:
† 200 strains of actinomycetes associated with
cave paintings in various crypts, caves, and
tombs (Giacobini et al. 1987);
† 350 taxa of actinomycetes identified from
Altamira Cave, Spain (Groth & Saiz-Jimenez
1999);
†
Streptomyces (8 strains), Bacillus (4 strains),
Nocardiopsis (3 strains) and various other taxa
found inGrotto deoCervi, Italy (Laiz et al. 2000);
† 38 phylotypes related to Ortobacteria, Actino-
bacteria, and Cytophagales in Glenwood
Caverns, Colorado (Barton et al. 2004); and
† 12 bacterial divisions and subdivisions compris-
ing 49 phylotypes identified in samples collected
from Wind Cave in South Dakota, U.S.A.
(Chelius & Moore 2004).
These examples, based on chemotaxonomic
techniques, further emphasize the tremendous diver-
sity of microbes that can thrive in caves. Most new
taxa of cave microbes are now defined solely on
the basis of their chemotaxonomic attributes. Lee
(2006), for example, defined a new species of actino-
mycetes from a cave on Jeju Island, Korea on the
basis of its 16S rRNA signature but he described it
as being '... a well-developed and branched sub-
strate mycelium that fragments into rod-shaped
Microbes in caves
Biotic composition and diversity
Barton & Northup (2007) suggested that any discus-
sion on microbes in caves should be split into two
eras that they centered on the 'Breakthroughs in
Karst Geomicrobiology and Redox Geochemistry'
conference held in 1994 (Sasowsky & Palmer
1994). That date coincides roughly with the advent
of new microbiological techniques, such as 16S
rDNA gene sequencing, which changed the
manner in which microbes were characterized and
classified and showed that cave biotas were far
more diverse than previously suspected.
The presence of microbes in caves has long been
recognized. Claus (1955), for example, noted that
Scopoli (1772), Humboldt (1793) and Hoffman
(1811) referred to fungi in caves, but unfortunately
failed to include these citations in his reference
list. Irrespective, many studies between 1900 and
1994 reported diverse microbial populations from
caves
throughout
the world,
including
the
following:
† bacteria, fungal hyphae and cyanohycea from
caves in Norway (Høeg 1946);
† various species of bacteria from caves in south
Wales (Mason-Williams 1959);
† 69 species, varieties and forms of algae from
Baradla cave in north Hungary (Claus 1955);
† 93 species (including 58 cyanophytes) from
caves in Baranya district; 90 species from B´ke
Cave, 41 species from P´lv˜ lgy Cave, and 13
species from K˜ lyuk Cave, all being located in
Hungary (Palik 1960);
† bacteria, actinomycetes, and fungi from caves in
France (Caumartin 1963);
† 7 species of algae from Crystal Cave, Kentucky
(Nagy 1965);
† 27 taxa from Mammoth Cave, Kentucky (Jones
1965); and
† 30 species of algae and 45 species of bacteria
from caves in South Wales (Mason-Williams
1967).
These examples amply demonstrate the diversity
of microbes found in many different caves. Such
diversity was emphasized by Draganov (1977)
who compiled a list of 627 taxa of cave algae that
had been recorded between the end of the 19th
century and the time when he wrote his paper.
This diverse biota included representatives of the
Cyanophyta, Rhodophyta, Chlorophyta, Pyrrophyta
and Euglenophyta.
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